Sediment flushings of hydropower reservoirs are commonly performed to maintain water resource uses and ecosystem services, but may have strong impacts on fish communities. Despite the worldwide scope of this issue, very few studies report quantitative in situ evaluations of these impacts. In June 2012, the drawdown flushing of the Verbois reservoir (Rhône River) was performed and subsequent impacts on the fish community were assessed, both inside the reservoir (fish densities by hydroacoustic surveys) and downstream (short-term movement and survival of radio tracked adult fish). Results showed that after the flushing fish acoustic density decreased by 57% in the reservoir, and no recolonization process was observed over the following 16 months. Downstream of the dam, the global apparent survival of fish to the flushing was estimated at 74%, but differed between species. The nine-year delay from the previous flushing and thus the amount of sediments to remove were too stressful for the low-resilience fish community of the Rhône River. Alternative flushing schedules are discussed to reduce these impacts.